Organization Cipher: Tales of the Shadow Trainer
by Uzumaki7
Summary: The Organization Cipher continues to exist as Shadow Pokemon continue to exist. Its legacy is Naruto Uzumaki and he sets out toward the Pokemon Nations. A Note inside for you to understand and give me feedback. Menma exist too.


Title: *****Organization Cipher: Tales of the Shadow Trainer*****.

Author: Uzumaki7

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**A/N**: Okay people this is a major note for you to understand this story and give me some feedback before I truly get this story going so I don't make any mistakes on this even though I will make some for this story. The characterization for Naruto Uzumaki is s somewhat of an anti-hero, neither good entirely or evil entirely.

Naruto Uzumaki is the main character of the story but he is not alone. Alongside him is his Universal Counterpart Menma Uzumaki who is his twin brother in the story.

Following the 3rd and 6th Naruto Shippūden movie this story obtains the influence of each of these movies. From the 6th Menma exists and together, they left Konohagakure at a young age for reasons unknown. During their journey both would encounter the 3rd movie antagonist Hiruko and he would train them allow them to know his Kinjutsu, the Chimera Technique. Also a trait of the 6th too Naruto and Menma would kidnap shinobi who possessed Kekkei genkai and Secret Techniques. They would help Hiruko achieve the fifth Kekkei genkai and would complete the Immortality Ritual and become a "Perfect Immortal Ninja". Together they would usher the 4th Great Shinobi World War.

But with the Akatsuki's interference the world quickly becomes unstable and heads toward destruction when the Jūbi is resurrected. Hiruko who begins to see the demise of this world activates a Space-Time Rift and sends Naruto and Menma through it. This Jutsu allows them to enter the Pokémon Universe, however due to the complexion of the distortion of Space-Time both Naruto and Menma were separated into different regions. Naruto would be the one to enter the Ōre Region.

Two years had passed since Naruto entered the Ōre Region and would become a part of a small organization called "Team Snag 'em". Team Snag 'em was an organization within the Ōre Region that stole other trainers Pokémon by using a mechanism convert average "PokeBalls" into "SnagBalls" and allow the members of Team Snag 'em capable of stealing other trainers Pokémon even when they were owned by someone. This technology was called the "Snag-Machine". Naruto and another trainer named Wes (Leo in Japanese) were the highest capable members that stole other people's Pokémon.

Both held no higher reason for the organization they were a part of and would team up and become two rogue trainers of their organization. They would destroy the Snag-Machine that turned PokeBalls into SnagBalls and would take the "Portable Snag-Machine" and travel through the Ōre Region and quickly be caught in the Distribution of Shadow Pokémon. The other organization that worked alongside the petty organization "Team Snag 'em" was the organization called "Cipher". Cipher was the major cause that would not only lead the distribution of Shadow Pokémon, but would also be responsible for the crime that would plague the Ōre Region. The organization would gain the Pokémon from Team Snag 'em stole and turn them into Shadow Pokémon.

In their goal of conquest they were capable of having Pokémon shut their hearts and become ruthless "Fighting Machines". This is the concept due to the fact Shadow Pokémon: are virtually "Soulless" and will obey their master. Shadow Pokémon even show no standards to attack even humans, whether if it was an order or not. Knowing a Shadow Pokémon from an average Pokémon is from an ominous purple aura that surrounds it. An average human is not capable of seeing this aura unless one possesses the "gift" in seeing a Shadow Pokémon's Aura or an Aura Reader produced five years after the events of the Shadow Pokémon Incident.

A Shadow Pokémon is incredibly powerful, being able to learn "Shadow Moves" that aren't limited to a type disadvantage. Everything about a Shadow Pokémon is brought to the very limit. Strength, speed and all other abilities are increased. But Shadow Pokémon are not invincible, they are still capable of being defeated.

Even with their power being at the very limit there is still a catch, despite these capabilities a Shadow Pokémon succumbs to a madness that will allow it to disobey its trainer and become complicated in battle. Due to them becoming Shadow Pokémon, they are incapable of evolving and are unable to learn new moves other than the moves they already knew before they turned into Shadow Pokémon.

But things are not lost for them. A Shadow Pokémon is capable of being restored but certain things must be needed in order to do that.

A Shadow Pokémon must need the power of Celebi; with a Time Flute a person is capable of summoning Celebi. Along with this the Shadow Pokémon must open its heart to its trainer. Because of Celebi's power of purity it will allow the Shadow Pokémon to recall its greatest and happiest memory. Along with its power the Shadow Pokémon will be restored. With all the experience it possessed during its time battling and gaining its heart it will be capable of evolving as well as learning new moves it was incapable of doing due to it being a Shadow Pokémon.

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><p>Journeying through the Ōre Region Naruto has two Pokémon companions with him since the beginning he entered the Ōre Region. Due to this one being a difficult one I chose a two Pokémon to be his companions and those two Pokémon are from the Eevee evolutionary line.<p>

Flareon, Vaporeon and Jolteon, these are the only choice and there can only be two.

Either it goes Flareon and Vaporeon, Vaporeon and Jolteon, or Flareon and Jolteon. Both are a reverse type disadvantage combo using fire and water, water and electric, or having fire and electric.

Espeon and Umbreon cannot be his Starter Pokémon due to Wes/Leo already having this duo. So I ask your choice on this.

The choice can still be different.

The idea of using two Ralts and having them turn into the duo, Gardevoir and Gallade. This is from the loyalty they would have toward their master and would not hesitate to give their lives for him even when his motives are considered "Evil.

These two companions will not be Shadow Pokémon due to the principle Naruto has.

Being the cause of Cipher's destruction Naruto would take over the organization and give a new usefulness toward Shadow Pokémon. Unlike it being the one to cause world domination Naruto seeks to use Shadow Pokémon to their highest potential and bring about a new order which side the world wants, the light or the shadow. With some of the negations Cipher had done Naruto would stumble upon the DarkBalls. Using these he would create more and then venture out toward the Pokémon Nations to perform his 'experiment' onto the world and test the possibilities with Shadow Pokémon.

The DarkBalls are the instruments to another form of Shadow Pokémon and truly become evil. Performing the same qualities as the SnagBall itself and performing the same qualities as the Shadow Pokémon when they turn these are the reason for Naruto being capable of turning Pokémon he captures into Shadow Pokémon.

The Ōre Region itself is a melting pot, containing the Pokémon from Kanto, Johto and Hoenn. Pokémon are not native to the region and are imported or smuggled into the region. With that, Naruto is capable of going to any of the three regions with choice.

My choice is Hoenn.

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><p>Now Naruto's Kekkei genkai, while I did make plans to explain, I will do that in the actual serious chapter. I ask you what your choices are, the limitation he has is three to four Kekkei genkai. There is no OP to this, the Sharingan, Mokuton and Rinnegan are not allowed into this story and only the lesser Kekkei genkai are allowed.<p>

So I ask you to please review and give me some feedback. Thank you and do not hesitate to ask or question, I will take ideas into consideration. And talk about the pairing to, I am curious before I get to what I was thinking about.


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